Brain data#

This section presents results of brain MRI data. Below are quantitative T1 values computed using the MP2RAGE and the MTsat methods. These values are averaged within the gray matter and white matter masks.

Gray matter qMRI#

Code imports#

# Python imports 
from IPython.display import clear_output
from pathlib import Path
import numpy as np
import pandas as pd

# Import custom tools
from tools.data import Data
from tools.plot import Plot

Download data#

data_type = 'brain'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)
--2022-06-14 04:16:44--  https://github.com/courtois-neuromod/anat-processing/releases/download//r20210726/neuromod-anat-brain-qmri.zip
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Load data plot it#

dataset.load()
fig_gm = Plot(dataset, plot_name = 'brain-1')

fig_gm.title = 'Brain gray matter qMRI microstructure'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_gm.display('jupyter-book', tissue = 'GM')
[[1.4885, 1.4651, 1.285, -100], [1.4674, 1.4598, 1.4625, 1.4542], [1.4929, 1.4977, -100, 1.4964], [1.315, 1.2597, 1.2551, -100], [1.4773, 1.4801, -100, -100], [-100, -100, -100, 1.3065]]
MP2RAGE
[[1.7582, 1.7805, 1.5235, -100], [1.8387, 1.7777, 1.6814, 1.6291], [1.7867, 1.83, -100, 1.7999], [1.4853, 1.3929, 1.4778, -100], [1.9455, 1.8808, -100, -100], [-100, -100, -100, 1.5384]]
MTS
[[45.3931, 45.6771, 38.2974, -100], [46.4224, 46.9693, 47.0274, 46.8317], [45.5349, 45.5003, -100, 46.3153], [40.8195, 39.712, 41.6998, -100], [46.8891, 46.6286, -100, -100], [-100, -100, -100, 40.6206]]
MTR
[[2.6791, 3.2149, 8.3607, -100], [2.1697, 2.4692, 4.4383, 3.8181], [1.9555, 1.9462, -100, 2.3336], [4.6358, 4.9702, 12.5801, -100], [2.2007, 2.1552, -100, -100], [-100, -100, -100, 8.5125]]
MTsat
[[1.4885, 1.4651, 1.285, -100], [1.4674, 1.4598, 1.4625, 1.4542], [1.4929, 1.4977, -100, 1.4964], [1.315, 1.2597, 1.2551, -100], [1.4773, 1.4801, -100, -100], [-100, -100, -100, 1.3065]]
[[1.7582, 1.7805, 1.5235, -100], [1.8387, 1.7777, 1.6814, 1.6291], [1.7867, 1.83, -100, 1.7999], [1.4853, 1.3929, 1.4778, -100], [1.9455, 1.8808, -100, -100], [-100, -100, -100, 1.5384]]
[[45.3931, 45.6771, 38.2974, -100], [46.4224, 46.9693, 47.0274, 46.8317], [45.5349, 45.5003, -100, 46.3153], [40.8195, 39.712, 41.6998, -100], [46.8891, 46.6286, -100, -100], [-100, -100, -100, 40.6206]]
[[2.6791, 3.2149, 8.3607, -100], [2.1697, 2.4692, 4.4383, 3.8181], [1.9555, 1.9462, -100, 2.3336], [4.6358, 4.9702, 12.5801, -100], [2.2007, 2.1552, -100, -100], [-100, -100, -100, 8.5125]]
[[   1.4885    1.4651    1.285  -100.    ]
 [   1.4674    1.4598    1.4625    1.4542]
 [   1.4929    1.4977 -100.        1.4964]
 [   1.315     1.2597    1.2551 -100.    ]
 [   1.4773    1.4801 -100.     -100.    ]
 [-100.     -100.     -100.        1.3065]
 [   1.7582    1.7805    1.5235 -100.    ]
 [   1.8387    1.7777    1.6814    1.6291]
 [   1.7867    1.83   -100.        1.7999]
 [   1.4853    1.3929    1.4778 -100.    ]
 [   1.9455    1.8808 -100.     -100.    ]
 [-100.     -100.     -100.        1.5384]]
[[   1.4885    1.4651    1.285  -100.    ]
 [   1.4674    1.4598    1.4625    1.4542]
 [   1.4929    1.4977 -100.        1.4964]
 [   1.315     1.2597    1.2551 -100.    ]
 [   1.4773    1.4801 -100.     -100.    ]
 [-100.     -100.     -100.        1.3065]
 [   1.7582    1.7805    1.5235 -100.    ]
 [   1.8387    1.7777    1.6814    1.6291]
 [   1.7867    1.83   -100.        1.7999]
 [   1.4853    1.3929    1.4778 -100.    ]
 [   1.9455    1.8808 -100.     -100.    ]
 [-100.     -100.     -100.        1.5384]]
[[45.3931, 45.6771, 38.2974, -100], [46.4224, 46.9693, 47.0274, 46.8317], [45.5349, 45.5003, -100, 46.3153], [40.8195, 39.712, 41.6998, -100], [46.8891, 46.6286, -100, -100], [-100, -100, -100, 40.6206]]
[[45.3931, 45.6771, 38.2974, -100], [46.4224, 46.9693, 47.0274, 46.8317], [45.5349, 45.5003, -100, 46.3153], [40.8195, 39.712, 41.6998, -100], [46.8891, 46.6286, -100, -100], [-100, -100, -100, 40.6206]]
[[2.6791, 3.2149, 8.3607, -100], [2.1697, 2.4692, 4.4383, 3.8181], [1.9555, 1.9462, -100, 2.3336], [4.6358, 4.9702, 12.5801, -100], [2.2007, 2.1552, -100, -100], [-100, -100, -100, 8.5125]]
[[2.6791, 3.2149, 8.3607, -100], [2.1697, 2.4692, 4.4383, 3.8181], [1.9555, 1.9462, -100, 2.3336], [4.6358, 4.9702, 12.5801, -100], [2.2007, 2.1552, -100, -100], [-100, -100, -100, 8.5125]]
[[   1.4885    1.4651    1.285  -100.    ]
 [   1.4674    1.4598    1.4625    1.4542]
 [   1.4929    1.4977 -100.        1.4964]
 [   1.315     1.2597    1.2551 -100.    ]
 [   1.4773    1.4801 -100.     -100.    ]
 [-100.     -100.     -100.        1.3065]
 [   1.7582    1.7805    1.5235 -100.    ]
 [   1.8387    1.7777    1.6814    1.6291]
 [   1.7867    1.83   -100.        1.7999]
 [   1.4853    1.3929    1.4778 -100.    ]
 [   1.9455    1.8808 -100.     -100.    ]
 [-100.     -100.     -100.        1.5384]]
[[   1.4885    1.4651    1.285  -100.    ]
 [   1.4674    1.4598    1.4625    1.4542]
 [   1.4929    1.4977 -100.        1.4964]
 [   1.315     1.2597    1.2551 -100.    ]
 [   1.4773    1.4801 -100.     -100.    ]
 [-100.     -100.     -100.        1.3065]
 [   1.7582    1.7805    1.5235 -100.    ]
 [   1.8387    1.7777    1.6814    1.6291]
 [   1.7867    1.83   -100.        1.7999]
 [   1.4853    1.3929    1.4778 -100.    ]
 [   1.9455    1.8808 -100.     -100.    ]
 [-100.     -100.     -100.        1.5384]]

White matter qMRI#

fig_wm = Plot(dataset, plot_name = 'brain-2')

fig_wm.title = 'Brain white matter qMRI microstructure'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_wm.display('jupyter-book', tissue = 'WM')
[[0.94136, 0.9462, 1.0346, -100], [0.90359, 0.90871, 0.90185, 0.90232], [0.88612, 0.88218, -100, 0.88721], [0.97833, 0.9795, 0.968, -100], [0.91238, 0.90486, -100, -100], [-100, -100, -100, 0.96392]]
MP2RAGE
[[1.0207, 1.0348, 1.0475, -100], [1.021, 1.0044, 0.99252, 0.96173], [0.97915, 0.9999, -100, 1.036], [1.0128, 0.96615, 1.028, -100], [1.0388, 1.0421, -100, -100], [-100, -100, -100, 1.0122]]
MTS
[[54.0544, 54.1103, 53.2875, -100], [54.2992, 54.1307, 54.2658, 54.3671], [54.5125, 54.7791, -100, 55.1095], [53.5777, 53.4147, 54.3775, -100], [54.8262, 54.5027, -100, -100], [-100, -100, -100, 53.0978]]
MTR
[[5.0026, 4.7489, 8.4598, -100], [4.3271, 4.3393, 4.5628, 5.1863], [4.4926, 4.3475, -100, 4.4228], [5.9779, 5.9091, 6.6724, -100], [5.1489, 4.3173, -100, -100], [-100, -100, -100, 8.5528]]
MTsat
[[0.94136, 0.9462, 1.0346, -100], [0.90359, 0.90871, 0.90185, 0.90232], [0.88612, 0.88218, -100, 0.88721], [0.97833, 0.9795, 0.968, -100], [0.91238, 0.90486, -100, -100], [-100, -100, -100, 0.96392]]
[[1.0207, 1.0348, 1.0475, -100], [1.021, 1.0044, 0.99252, 0.96173], [0.97915, 0.9999, -100, 1.036], [1.0128, 0.96615, 1.028, -100], [1.0388, 1.0421, -100, -100], [-100, -100, -100, 1.0122]]
[[54.0544, 54.1103, 53.2875, -100], [54.2992, 54.1307, 54.2658, 54.3671], [54.5125, 54.7791, -100, 55.1095], [53.5777, 53.4147, 54.3775, -100], [54.8262, 54.5027, -100, -100], [-100, -100, -100, 53.0978]]
[[5.0026, 4.7489, 8.4598, -100], [4.3271, 4.3393, 4.5628, 5.1863], [4.4926, 4.3475, -100, 4.4228], [5.9779, 5.9091, 6.6724, -100], [5.1489, 4.3173, -100, -100], [-100, -100, -100, 8.5528]]
[[   0.94136    0.9462     1.0346  -100.     ]
 [   0.90359    0.90871    0.90185    0.90232]
 [   0.88612    0.88218 -100.         0.88721]
 [   0.97833    0.9795     0.968   -100.     ]
 [   0.91238    0.90486 -100.      -100.     ]
 [-100.      -100.      -100.         0.96392]
 [   1.0207     1.0348     1.0475  -100.     ]
 [   1.021      1.0044     0.99252    0.96173]
 [   0.97915    0.9999  -100.         1.036  ]
 [   1.0128     0.96615    1.028   -100.     ]
 [   1.0388     1.0421  -100.      -100.     ]
 [-100.      -100.      -100.         1.0122 ]]
[[   0.94136    0.9462     1.0346  -100.     ]
 [   0.90359    0.90871    0.90185    0.90232]
 [   0.88612    0.88218 -100.         0.88721]
 [   0.97833    0.9795     0.968   -100.     ]
 [   0.91238    0.90486 -100.      -100.     ]
 [-100.      -100.      -100.         0.96392]
 [   1.0207     1.0348     1.0475  -100.     ]
 [   1.021      1.0044     0.99252    0.96173]
 [   0.97915    0.9999  -100.         1.036  ]
 [   1.0128     0.96615    1.028   -100.     ]
 [   1.0388     1.0421  -100.      -100.     ]
 [-100.      -100.      -100.         1.0122 ]]
[[54.0544, 54.1103, 53.2875, -100], [54.2992, 54.1307, 54.2658, 54.3671], [54.5125, 54.7791, -100, 55.1095], [53.5777, 53.4147, 54.3775, -100], [54.8262, 54.5027, -100, -100], [-100, -100, -100, 53.0978]]
[[54.0544, 54.1103, 53.2875, -100], [54.2992, 54.1307, 54.2658, 54.3671], [54.5125, 54.7791, -100, 55.1095], [53.5777, 53.4147, 54.3775, -100], [54.8262, 54.5027, -100, -100], [-100, -100, -100, 53.0978]]
[[5.0026, 4.7489, 8.4598, -100], [4.3271, 4.3393, 4.5628, 5.1863], [4.4926, 4.3475, -100, 4.4228], [5.9779, 5.9091, 6.6724, -100], [5.1489, 4.3173, -100, -100], [-100, -100, -100, 8.5528]]
[[5.0026, 4.7489, 8.4598, -100], [4.3271, 4.3393, 4.5628, 5.1863], [4.4926, 4.3475, -100, 4.4228], [5.9779, 5.9091, 6.6724, -100], [5.1489, 4.3173, -100, -100], [-100, -100, -100, 8.5528]]
[[   0.94136    0.9462     1.0346  -100.     ]
 [   0.90359    0.90871    0.90185    0.90232]
 [   0.88612    0.88218 -100.         0.88721]
 [   0.97833    0.9795     0.968   -100.     ]
 [   0.91238    0.90486 -100.      -100.     ]
 [-100.      -100.      -100.         0.96392]
 [   1.0207     1.0348     1.0475  -100.     ]
 [   1.021      1.0044     0.99252    0.96173]
 [   0.97915    0.9999  -100.         1.036  ]
 [   1.0128     0.96615    1.028   -100.     ]
 [   1.0388     1.0421  -100.      -100.     ]
 [-100.      -100.      -100.         1.0122 ]]
[[   0.94136    0.9462     1.0346  -100.     ]
 [   0.90359    0.90871    0.90185    0.90232]
 [   0.88612    0.88218 -100.         0.88721]
 [   0.97833    0.9795     0.968   -100.     ]
 [   0.91238    0.90486 -100.      -100.     ]
 [-100.      -100.      -100.         0.96392]
 [   1.0207     1.0348     1.0475  -100.     ]
 [   1.021      1.0044     0.99252    0.96173]
 [   0.97915    0.9999  -100.         1.036  ]
 [   1.0128     0.96615    1.028   -100.     ]
 [   1.0388     1.0421  -100.      -100.     ]
 [-100.      -100.      -100.         1.0122 ]]